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I fail to see anything wrong with such behavior, it looks flexible and user friendly to me. VirtualBox uses HOME if it's set USERPROFILE if it's set or as a final fallback %HOMEDRIVE%%HOMEPATH%. Could you state explicitly what you consider a bug here?

In my case I have set the HOME variable to my MSYS home folder and was surprised when I saw VirtualBox creating a VHD in there.
I did not expect any Windows application making use of the HOME variable.

I would consider this to be more of a usability issue than a bug though.

This explains why all of a sudden I lost all my VB settings, %HOME% is now getting ignored. Perhaps such changes should not be made in minor releases and instead they should be reserved for more major upgrades, I upgraded from .20 to .22 and all my settings were gone.